Figure Legends
Figure 1: The relative abundance of WHY1 transcripts in the base, middle and tip sections of the first leaf of 7-day old wild type seedlings estimated by qRT-PCR (A) and Western blot (B). Data in panel A are presented as means ± SE (n = 3).  Different letters represent statistical differences assessed by One-way ANOVA followed by Tukey’s post hoc  test.
Figure 2: Distribution of WHY1 in barley leaf determined by immunogold labelling. Leaf sections were prepared for immunogold labelling and the presence of WHY1 detected by ployclonol antibody as described. Images are representative of plastids (p) in the leaf base (A); chloroplasts (c) in the leaf tip (B); nucleus with nucleolus (nu) in the leaf base (m, mitochondrion) (C) and a detail of the nucleus in the leaf base (D). Example gold particles are indicated by white arrows. Scale bars representing 0.5 (A, B, D) or 1 µm (C) are provided in individual panels.
Figure 3: Cluster analysis comparison of abundance of transcripts that differ significantly in the base, middle and tip regions of wild type 7-day old barley leaves. Relative transcript abundance is represented according to the legend shown. Transcripts were grouped in clusters (A-E) as indicated and are ordered as listed in table S1.
Figure 4: Cluster analysis comparison of abundance of key transcripts that show a developmental pattern of expression in the base, middle and tip regions of wild type, W1-1 and W1-7 barley leaves. Relative transcript abundance is represented according to the legend shown. Transcripts mentioned in the text are indicated and other transcripts are ordered as indicated in table S3.
Figure 5: Cluster analysis comparison of abundance of transcripts associated with light signalling and plastid development exhibiting significant differences in abundance in base, middle and tip regions of wild type 7 day old barley leaves. Relative transcript abundance is represented according to the legend shown. Gene accession numbers are indicated to the right of each row and further details are provided in table S4.
Figure 6: Cluster analysis comparison of abundance of transcripts associated with plastid biogenesis and development exhibiting significant differences in abundance in the base of wild type, W1-1 and W1-7 7 day old barley leaves. Relative transcript abundance is represented according to the legend shown. Transcripts are ordered as indicated in Table S6.
Figure 7: Polar and non-polar metabolites exhibiting significant differences in abundance in base, middle and tip regions of wild type 7 day old barley leaves. Abundance is shown relative to basal regions for each compound where bars represent mean and lines SE (n=4). ■, base; □, middle; ■, tip. C14:0, tetradecanoic acid; C17:0, heptacanoic acid; C22 alc, docosanol; C24 alc, tetracosanol.
Figure 8: Relative abundance of transcripts associated with primary metabolism (A) and primary metabolites (B) exhibiting significant differences in abundance in the basal region of 7-day old wild type and WHY1 knockdown barley leaves.
Figure 9: Western blots of selected chloroplast proteins in the base, middle and tip sections of the first leaves of wild type (WT) and W1-1 and W1-7 of seedlings 7 days after germination. Proteins detected are chlorophyll a/b-binding proteins: LHCB1 and LHCB2, the small subunit of RUBISCO (RBCS), chloroplast ribosomal protein S1 (RPS1), , the large subunit of RUBISCO (RBCL), the photosystem II protein (D1) and WHIRLY1 (WHY1).
Figure S1: Representative transmission electron micrographs of nucleus in base of WT barley leaves indicating the association of WHY1 protein (red arrows) with electron dense chromatin (Ch).
Figure S2: A comparisons of leaf chlorophyll content in the base, middle and tip sections of the first leaves of 7-day old wild type (WT), W1-1 and W1-7 seedlings. Data are presented as mean ± SE (n = 6).  Different letters represent statistical differences assessed by one-way ANOVA followed by Tukey’s post hoc  test.